docs: refresh tutorials, how-to, design, reference, and examples for v0.4.0

Pre-cut documentation pass for the 0.4.0 release, verified against current source.

Corrections:
- fipsctl: stale 'show identities'/'show node' -> 'show status'
  (host-a-service, run-as-unprivileged-user)
- mesh address derivation: first 16 bytes of SHA-256(pubkey) with the leading
  byte set to 0xfd, not a fixed fd97: prefix (reach-mesh-services,
  ipv6-adapter-walkthrough)
- gateway control socket mode 0660 -> 0770 (troubleshoot-gateway)
- Tor example: add advertised_port: 8443 so the published port matches the
  prose (enable-nostr-discovery)
- bloom mesh-size estimate rewritten to the OR-union-of-peer-filters algorithm;
  plus mtu deep-link, gateway pool wording, and a NAT failure-mode line
- examples: delete orphaned nostr-rs-relay config, accept inbound to the local
  8443 TCP listener, fix fd::/8 -> fd00::/8 typos, dotless wireguard alias

Additions:
- new Nym mixnet transport section (fips-transport-layer) and the architecture
  transport list
- new LAN/mDNS discovery section (fips-nostr-discovery)
- reference docs: Nym transport, LAN discovery, and new control/stats surfaces;
  drop ble from the connect transport list

docs/design/fips-mtu.md

@@ -251,7 +251,7 @@ would later drop.
 The adapter integrates with the MTU subsystem rather than owning it.
 The "why we clamp and what `max_mss` means" lives here in the MTU
 design; the "how the clamp is implemented at the TUN" lives in the
-[IPv6 adapter](fips-ipv6-adapter.md#tcp-mss-clamping) doc.
+[IPv6 adapter](fips-ipv6-adapter.md#tun-side-tcp-mss-clamping) doc.
 
 ## ICMP Packet Too Big